Microbial succession and dynamics in meromictic Mono Lake, California

Transcriptomic insights into the dominance of two phototrophs throughout the water column of a tropical hypersaline-alkaline crater lake (Dziani Dzaha, Mayotte)

Saline-alkaline lakes often shelter high biomasses despite challenging conditions, owing to the occurrence of highly adapted phototrophs. Dziani Dzaha (Mayotte) is one such lake characterized by the stable co-dominance of the cyanobacterium Limnospira platensis and the picoeukaryote Picocystis salinarum throughout its water column. Despite light penetrating only into the uppermost meter, the prevailing co-dominance of these species persists even in light- and oxygen-deprived zones. Here, a depth profile of phototrophs metatranscriptomes, annotated using genomic data from isolated strains, is employed to identify expression patterns of genes related to carbon processing pathways including photosynthesis, transporters and fermentation. The findings indicate a prominence of gene expression associated with photosynthesis, with a peak of expression around 1 m below the surface, although the light intensity is very low and only red and dark red wavelengths can reach it, given the very high turbidity linked to the high biomass of L. platensis. Experiments on strains confirmed that both species do grow under these wavelengths, at rates comparable to those obtained under white light. A decrease in the expression of photosynthesis-related genes was observed in L. platensis with increasing depth, whereas P. salinarum maintained a very high pool of psbA transcripts down to the deepest point as a possible adaptation against photodamage, in the absence and/or very low levels of expression of genes involved in protection. In the aphotic/anoxic zone, expression of genes involved in fermentation pathways suggests active metabolism of reserve or available dissolved carbon compounds. Overall, L. platensis seems to be adapted to the uppermost water layer, where it is probably maintained thanks to gas vesicles, as evidenced by high expression of the gvpA gene. In contrast, P. salinarum occurs at similar densities throughout the water column, with a peak in abundance and gene expression levels which suggests a better adaptation to lower light intensities. These slight differences may contribute to limited inter-specific competition, favoring stable co-dominance of these two phototrophs.

In the right place, at the right time: the integration of bacteria into the Plankton Ecology Group model

BACKGROUND

Planktonic microbial communities have critical impacts on the pelagic food web and water quality status in freshwater ecosystems, yet no general model of bacterial community assembly linked to higher trophic levels and hydrodynamics has been assessed. In this study, we utilized a 2-year survey of planktonic communities from bacteria to zooplankton in three freshwater reservoirs to investigate their spatiotemporal dynamics.

RESULTS

We observed site-specific occurrence and microdiversification of bacteria in lacustrine and riverine environments, as well as in deep hypolimnia. Moreover, we determined recurrent bacterial seasonal patterns driven by both biotic and abiotic conditions, which could be integrated into the well-known Plankton Ecology Group (PEG) model describing primarily the seasonalities of larger plankton groups. Importantly, bacteria with different ecological potentials showed finely coordinated successions affiliated with four seasonal phases, including the spring bloom dominated by fast-growing opportunists, the clear-water phase associated with oligotrophic ultramicrobacteria, the summer phase characterized by phytoplankton bloom-associated bacteria, and the fall/winter phase driven by decay-specialists.

CONCLUSIONS

Our findings elucidate the major principles driving the spatiotemporal microbial community distribution in freshwater ecosystems. We suggest an extension to the original PEG model by integrating new findings on recurrent bacterial seasonal trends. Video Abstract.

Bacterial community structure in geothermal springs on the northern edge of Qinghai-Tibet plateau

Introduction:

In order to reveal the composition of the subsurface hydrothermal bacterial community in the zones of magmatic tectonics and their response to heat storage environments.

Methods:

In this study, we performed hydrochemical analysis and regional sequencing of the 16S rRNA microbial V4-V5 region in 7 Pleistocene and Lower Neogene hot water samples from the Gonghe basin.

Results:

Two geothermal hot spring reservoirs in the study area were found to be alkaline reducing environments with a mean temperature of 24.83°C and 69.28°C, respectively, and the major type of hydrochemistry was SO4-Cl·Na. The composition and structure of microorganisms in both types of geologic thermal storage were primarily controlled by temperature, reducing environment intensity, and hydrogeochemical processes. Only 195 ASVs were shared across different temperature environments, and the dominant bacterial genera in recent samples from temperate hot springs were Thermus and Hydrogenobacter, with both genera being typical of thermophiles. The correlation analysis showed that the overall level of relative abundance of the subsurface hot spring relied on a high temperature and a slightly alkaline reducing environment. Nearly all of the top 4 species in the abundance level (53.99% of total abundance) were positively correlated with temperature and pH, whereas they were negatively correlated with ORP (oxidation–reduction potential), nitrate, and bromine ions.

Discussion:

In general, the composition of bacteria in the groundwater in the study area was sensitive to the response of the thermal storage environment and also showed a relationship with geochemical processes, such as gypsum dissolution, mineral oxidation, etc.

A Novel and Sensitive Method for the Analysis of Fatty Acid Biosignatures by Capillary Electrophoresis-Mass Spectrometry

Fatty acids are a well-established class of compounds targeted as biosignatures for future missions to look for evidence of life on ocean worlds such as Europa and Enceladus. In order to establish their abiotic or biotic origin, we need to separate and quantify fatty acids to determine their relative abundances within a sample. In this study, we demonstrate the high potential of capillary electrophoresis coupled to mass spectrometry (CE-MS) for the efficient separation and sensitive detection of a wide variety of fatty acids. Three derivatization strategies were evaluated to allow the detection of fatty acids by positive ionization mode MS. Furthermore, CE-MS conditions were optimized to provide maximum separation efficiencies and detection sensitivities for the analysis of saturated and unsaturated fatty acids with even- and odd-numbered carbon chain lengths. Optimum separation and detection were obtained using a background electrolyte of 2 M acetic acid in 45% acetonitrile, after derivatization of the fatty acids with 2-picolylamine or N,N-diethylethylenediamine. The limits of detection for the derivatized fatty acids using the optimized method ranged from 25 to 250 nM. The optimized method was also used for the analysis of fatty acids in cell cultures and natural samples. Two distinctive biosignatures were obtained for the microorganisms Halobacillus halophilus and Pseudoalteromonas haloplanktis. In addition, multiple fatty acids were detected in a natural sample from Mono Lake, California.

Detection of Biosignatures by Capillary Electrophoresis Mass Spectrometry in the Presence of Salts Relevant to Ocean Worlds Missions

Capillary electrophoresis (CE) is a promising liquid-based technique for in situ chemical analysis on ocean worlds that allows the detection of a wide range of organic molecules relevant to the search for life. CE coupled with mass spectrometry (MS) is particularly valuable as it also enables the discovery of unknown compounds. Here we demonstrate that CE coupled to MS via electrospray ionization (ESI) can readily analyze samples containing up to half the saturation levels of salts relevant to ocean worlds when using 5 M acetic acid as the separation media. A mixture containing amino acids, peptides, nucleobases, and nucleosides was analyzed in the presence of two salts, NaCl and MgSO₄, based on their relevance to Europa and Enceladus. We demonstrate here CE-MS limits of detection for these organics ranging from 0.05 to 1 μM (8 to 89 ppb) in the absence of salts. More importantly, we demonstrate here for the first time that organics in the low micromolar range (1-50 μM) are detected by CE-MS in the presence of 3 M NaCl without desalting, preconcentration, or derivatization. This demonstration highlights how CE-MS is uniquely suited for organic analysis on future missions to ocean worlds.

Strong reorganization of multi-domain microbial networks associated with primary producers sedimentation from oxic to anoxic conditions in an hypersaline lake

Understanding the role of microbial interactions in the functioning of natural systems is often impaired by the levels of complexity they encompass. In this study, we used the relative simplicity of an hypersaline crater lake hosting only microbial organisms (Dziani Dzaha) to provide a detailed analysis of the microbial networks including the three domains of life. We identified two main ecological zones, one euphotic and oxic zone in surface, where two phytoplanktonic organisms produce a very high biomass, and one aphotic and anoxic deeper zone, where this biomass slowly sinks and undergoes anaerobic degradation. We highlighted strong differences in the structure of microbial communities from the two zones and between the microbial consortia associated with the two primary producers. Primary producers sedimentation was associated with a major reorganization of the microbial network at several levels: global properties, modules composition, nodes and links characteristics. We evidenced the potential dependency of Woesearchaeota to the primary producers' exudates in the surface zone, and their disappearance in the deeper anoxic zone, along with the restructuration of the networks in the anoxic zone toward the decomposition of the organic matter. Altogether, we provided an in-depth analysis of microbial association network and highlighted putative changes in microbial interactions supporting the functioning of the two ecological zones in this unique ecosystem.

Vertical structure of the bacterial diversity in meromictic Fayetteville Green Lake

The permanently stratified water columns in euxinic meromictic lakes produce niche environments for phototrophic sulfur oxidizers and diverse sulfur metabolisms. While Green Lake (Fayetteville, New York, NY) is known to host a diverse community of ecologically important sulfur bacteria, analyses of its microbial communities, to date, have been largely based on pigment analysis and smaller datasets from Sanger sequencing techniques. Here, we present the results of next-generation sequencing of the eubacterial community in the context of the water column geochemistry. We observed abundant purple and green sulfur bacteria, as well as anoxygenic photosynthesis-capable cyanobacteria within the upper monimolimnion. Amidst the phototrophs, we found other sulfur-cycling bacteria including sulfur disproportionators and chemotrophic sulfur oxidizers, further detailing our understanding of the sulfur cycle and microbial ecology of euxinic, meromictic lakes.